Add summits and remove extra names in files.

workflow/main.nf

@@ -342,6 +342,7 @@ process callPeaksMACS {
   output:
 
   set sampleId, file('*.narrowPeak'), file('*.fc_signal.bw'), file('*.pvalue_signal.bw'), experimentId, biosample, factor, treatment, replicate, controlId into experimentPeaks
+  file '*.xls' into summit
 
   script:
 

workflow/scripts/call_peaks_macs.py

@@ -125,7 +125,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
     # MACS2 sometimes calls features off the end of chromosomes.
     # Remove coordinates outside chromosome sizes
 
-    narrowpeak_fn = '%s_peaks.narrowPeak' % (prefix)
+    narrowpeak_fn = '%s.narrowPeak' % (prefix)
     clipped_narrowpeak_fn = 'clipped-%s' % (narrowpeak_fn)
 
 

workflow/tests/test_call_peaks_macs.py

@@ -12,7 +12,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 def test_call_peaks_macs_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.fc_signal.bw'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.pvalue_signal.bw'))
-    peak_file = test_output_path + 'ENCLB144FDT_peaks.narrowPeak'
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.xls'))
+    peak_file = test_output_path + 'ENCLB144FDT.narrowPeak'
     assert utils.count_lines(peak_file) == 227389
 
 
@@ -20,5 +21,6 @@ def test_call_peaks_macs_singleend():
 def test_call_peaks_macs_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.fc_signal.bw'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.pvalue_signal.bw'))
-    peak_file = test_output_path + 'ENCLB568IYX_peaks.narrowPeak'
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.xls'))
+    peak_file = test_output_path + 'ENCLB568IYX.narrowPeak'
     assert utils.count_lines(peak_file) == 112652